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Friday, June 17, 2016

The genetic structure of the world's first farmers (Lazaridis et al. 2016 preprint)

Huge one from the Laz at bioRxiv:

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

Very likely this is also the definite proof of my Italian Refugium of R1b1 (and I hope also of R1a) and much other. Someone says to some Ulixides that hg. J has nothing to do with Middle East, but arrived there not before 5000 years ago from Caucasus very likely (and that Italy and Europe have subclades long before Middle East). No surprise to me about Natufians.

Craniometric analyses have suggested that the Natufians may have migrated from north or sub-Saharan Africa 25,26 186, a result that finds some support from Y chromosome analysis which shows that the Natufians and successor Levantine Neolithic populations carried haplogroup E, of likely ultimate African origin, which has not been detected in other ancient males from West Eurasia (Supplementary Information, section 6) 7, 8, 189. However, no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians (Extended Data Table 1).

Seems the migration could have easily gone the other direction.

From Poznik et al 2016:

Consistent with previous proposals 14, a parsimonious interpretation of the phylogeny is that the predominant African haplogroup, haplogroup E, arose outside the continent. This model of geographical segregation within the CT clade requires just one continental haplogroup exchange (E to Africa), rather than three (D, C, and F out of Africa). Furthermore, the timing of this putative return to Africa—between the emergence of haplogroup E and its differentiation within Africa by 58 kya—is consistent with proposals, based on non–Y chromosome data, of abundant gene flow between Africa and nearby regions of Asia 50–80 kya15.

The tests with the Mota sample surprised me. The authors don't say too much, but if Mota actually had zero admixture at all from any of these Basal Eurasian or farming populations, that says something.

I think it is likely that there were much earlier 'back migrations' from the Basal Eurasian population to Africa. But without an actual ancient sample, they can't really say anything. The ghost population can work in some contexts, but I don't think it works when looking at back migrations to Africa from a Eurasian population.

"To the west, the early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians. This is consistent with an Anatolian origin of farming in Europe, but does not reject other sources, since the spatial distribution of the Anatolian/European-like farmer populations is unknown [p. 8]."We can rule out the hypothesis that European farmers stem directly from a population related to the ancient farmers of the southern Levant, however, since they share more allele with Anatolian Neolithic farmers than with Levantine farmers as attested by the positive statistic f4(Europe_EN, Chimp; Anatolia_N, Levant_N) (Z=15) [pp- 8-9]."Previously, the West Eurasian population known to be the best proxy for this ancestry was present-day Sardinians, who resemble Neolithic Europeans genetically. However, our analysis shows that East African ancestry is significantly better modelled by Levantine early farmers than by Anatolian or early European farmers, implying that the spread of this ancestry to East Africa was not from the same group that spread Near Eastern ancestry into Europe (Extended 283 Data Fig. 4; Supplementary Information, section 8)" [p. 9]."We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe; all sampled South Asian groups are inferred to have significant amounts of both ancestral types. The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian population with minimal ANI along the ‘Indian Cline’ of such ancestry is inferred to have ~18% steppe-related ancestry, while the Kalash of Pakistan are inferred to have ~50%, similar to present-day northern Europeans". "Northwest Anatolians—with ancestry from a population related to European hunter-gatherers (Supplementary Information, section 7)—are better modelled if this ancestry is taken as more extreme than Bichon (Supplementary Information, section 10)" [p. 10].

But Levantinists and Stanford's Leftists persist: "The population structure of the ancient Near East was not independent of that of Europe (Supplementary Information, section 4), as evidenced by the highly significant (Z=-8.9) statistic f4(Iran_N, Natufian;WHG, EHG) which suggests gene flow in ‘northeastern’ (Neolithic Iran/EHG) and ‘southwestern’ (Levant/WHG) interaction spheres (Fig. 4d). This interdependence of the ancestry of Europe and the Near East may have been mediated by unsampled geographically intermediate populations that contribute ancestry to both regions" [p.10].

The mtDNA results were all expected. 99.9% of West Eurasian mtDNA that isn't U(xK, U1, U3, U7, U9) is Middle Eastern. No more pet-theories about loads of mtDNA H hiding in some Paleolithic gravesite in Spain.

Unlike Anatolia_Neolithic, the new Neolithic Middle Eastern mtDNAs don't belong to European-specific subclades. N1b, R0a(inclu. R0a2), T1a2, and H14a in Neolithic Levant are all most typical of modern Levant/SouthWest Asia today.

U7a appeared in Neolithic Iran and is today most popular in Iran(and also has a strong presence in South Asia). U3a has been found in Neolithic Iran, Neolithic Anatolia, and Chalothic Armenia and is today most typical of West Asia(specifcally Levant) but also has presence in Europe.

Important small details about mtDNA links between Chalolithic Iran/Aremenia and Bronze age Europe that didn't exist in Europe during Neolithic. It's been obvious these are CHG lineages for a while and now we have good confirmation.

>mtDNA I1(specf. I1c) >T1a1'3>H2a1: Also appeared in Chalolithic Samara Russia. No doubt a CHG lineage.

Also mtDNA U4a, typical of EHG, was in one of the Chalolithic Armenians.

"farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia."

"Important small details about mtDNA links between Chalolithic Iran/Aremenia and Bronze age Europe that didn't exist in Europe during Neolithic. It's been obvious these are CHG lineages for a while and now we have good confirmation. "

You're ignoring the part where they say "related to". The genetic structure in Iran changes from the Neolithic to the Chalcolithic, so Iran wasn't the source of the Iranian-like admixture on the steppe.

Also, unless women spread Indo-European languages onto the steppe, then the population that migrated both to the steppe and Chalcolithic Iran wasn't Indo-European. That's because there are no Y-HG J or G in any elite Kurgans, not even in one.

CHG admixture didn't enter Yamnaya via a female market stretching 100s of miles. That's impossible considering they barely had wheels and horses. A large percentage, maybe as many as women, of Yamnaya's CHG ancestors were men. It looks like admixture was sex bias but it wasn't as sex bias as Y DNA would suggest.

No one predicted that 8,000 years ago R1b/a were the primary haplogroups in Russia, while J(2?) and L1a dominated Iran and G2a2 dominated Turkey. Instead Iran and Turkey were thought to be the source of modern R1a/b. Papers based on Y DNA were wrong because often modern mtDNA can't tell us anything about the distant origins of haplogroups.

First, the Mesolithic individual from Iran belonged to haplogroup J. This has also beendetected in two hunter-gatherers from the Upper Paleolithic in Georgia11, as well as in ahunter-gatherer from Karelia in northwest Russia5, suggesting that it had a widespread earlydistribution prior to the spread of farming with which its current distribution was initiallyassociated12. While the hunter-gatherers from Georgia resemble the one from Iran (Fig. 1b),their whole genome data shows very different patterns from the Eastern European huntergathererwho also possessed this haplogroup, as well as from a singleton Anatolian earlyfarmer who belonged to haplogroup J2a5. This should serve as a note of caution against theidea that Y-chromosome lineages can be thought as markers of populations and populationmovements

"While the Early/Middle Bronze Age ‘Yamnaya’-related group (Steppe_EMBA) is a good geneticmatch (together with Neolithic Iran) for ANI, the later Middle/Late Bronze Age steppe population(Steppe_MLBA) is not."

"So the R1a/R1b men buried with weapons and sacrificial offerings, even human in many cases, were not elites"

Which R1a/ R1b men are you talking about specifically.? There are many such people. If you are referring to Yamnaya : then not many at all, actually. Some ochre, temple rings, few had wagons, but mostly those in or near Majkop. The latter of which certainly ha chiefly kurgans with lost of weapons and metal.

If you're talking about CWC, then yes. But it's all very Copper Age Europe stuff: axes, arrows, etc.

Guess the answer to my question when Natufian DNA is coming was: tomorrow!!!

Still a bit unclear exactly how close the E1b1 Levantines are to the G2a Anatolians. It looks like they're on opposing sides of a still quite tight cluster, while the Zagros farmers are distinct. Admittedly I expected G2a in the Levantines, though I guess it could still pop-up in contemporaneous sites nearby, perhaps on the coast.

I want to see which modern populations fall between them on the otherwise empty part of the PCA they allude to, though of course it is obvious! One of the clearest PCAs by the way, where everything is nice and square and just "makes sense."

There are numerous cases where the language of the females becomes dominant eventually. English is the best example against both the Scandinavian males and French speaking Normans.

But in almost all such cases females are resident natives. It is very rare that migrating females carry the language in the patriarchy-dominated Eurasian continent.

In the case of Polynesians the language appears more closely related to the females. But their male counterparts are not entirely absent. In fact in some Polynesian islands O's are the majority instead of C1b.

But Kurgan burials may preserve the dead better than other forms. The most notable practice in the steppe is an open burial where the dead are left on open(usually high) grounds. Cremation is another. The latter two obviously preserve the remains less well. Kurgan remains may not faithfully represent the population under investigation.

"The mtDNA results were all expected. 99.9% of West Eurasian mtDNA that isn't U(xK, U1, U3, U7, U9) is Middle Eastern. No more pet-theories about loads of mtDNA H hiding in some Paleolithic gravesite in Spain".

Let's wait. I wrote about mt in Europe and Italy even more than about the Y. I'll study those haplotypes, but be warning that these theories of some friends of yours end up as their theories about Y R1b from Middle East!

Your hopes and dreams are based on the assumption that Central Asia was populated by almost identical Yamnaya-like populations as Eastern Europe, with loads of EASTERN EUROPEAN HUNTER-GATHERER ancestry.

There's no chance of that. You know why? Because Central Asia is not Eastern Europe.

Those Steppe EMBA for lot of those South Asian groups are greatly inflated lol and more related to Yamnaya than the Indo Iranian steppe hmm. Mala with 20% steppe ancestry , come on now lol. As per the paper EHG is defined as a mix of WHG and a population on the Onge/Han cline. They really need genomes from Central/South Asia to explain away the high levels of ANE there, because the Zagros Farmer is mostly Basal.

oK. Lets go to first base. Im trying to understand the Near East deal.

The first issue is the correlation of Basal Eurasian, no Neanderthal admixture, and trying to piece that into what we thought - AMHs first encountered Nanderthals exactly in the Near East.

So it means that BE came from somewhere further south, after the LGM. But it had no signs of sub-saharan admixture, and is not earlier or more basal in the Levant than Iran. Given that there is clear attestation of a recent back-migration into Africa from a south Levantine population, it seems likely that the Basal Eurasian came from a refuge somewhere near the Persian Gulf.

Again, the lack of ANE in Mesolithic Iran must mean that wherever ANE came from, it wasn;t too close to the Zagros.

"Given that there is clear attestation of a recent back-migration into Africa from a south Levantine population"

True that there was a back migrations, but it could have been a back and forth for a long time.

There are not enough samples to say much at all.

Various Basal Eurasian lineages could have been all over North Africa until say, 20,000-15,000 years ago. After that time, SSA groups could have migrated in, only to be again largely replaced by a Eurasian back-migration. And then a Neolithic migration moved in as well.

For upper caste NW South Asians , I am sure there will be a substantial amount of Indo Iranian steppe admixture BUT , if you look at groups like Mala, Baloch ,Brahui with 20-33% , that is illogical for them to have that much Indo-Iranian admix , that "steppe" like ancestry is coming from else where.

''Admixture did not only occur within the Near East but extended towards Europe. To the266 north, a population related to people of the Iran Chalcolithic contributed ~43% of the267 ancestry of early Bronze Age populations of the steppe.''

"True that there was a back migrations, but it could have been a back and forth for a long time.

There are not enough samples to say much at all.

Various Basal Eurasian lineages could have been all over North Africa until say, 20,000-15,000 years ago. After that time, SSA groups could have migrated in, only to be again largely replaced by a Eurasian back-migration. And then a Neolithic migration moved in as well.

There is just no way to know at this point."

Yes, im not pretending to know what occurred in northern Africa over the eons, but rather the B.E. in Neolithic Europe & the Near East. If Iran Neolithic & Levant Neolithic are equidistant to it, then it probably came from between the two, rather than from one to the other. Or is that too simple ?

@davidskyIt would be more convincing if the remains from accidental deaths also yielded mostly R1a/R1b males.

Typical patrilineal societies exchange females between tribes while male lines are preserved(the very definition of 'patrilineal'). If one is buried in kurgan style while the other practiced cremation, archaeologists will only find the ones from kurgans, and someone like you will jubilate. "Aha I only see 'European' male lines while some of the female lines are from ***."

But in fact the tribe that practiced cremation had exactly the opposite pattern. Their male lines are almost entirely *** while some female lines are of European origins.

All modern populations are results of admixture. Even if South Asians are patrilineally European partially, that does not mean they are any more hybrids or are more illegitimate than Eastern Europeans who are also results of admixture in different patterns.

@mickeydodds,"Does this put to an end, once and for all, the endless debating of whether y DNA haplotype E1 is ultimately African or Eurasian in provenance?"

These Neolithic Levant guys specifically appeared to have had E1b-M123 not a basal form of E. E1b-M123 existing in the Levant in 10,000 BC is as good evidence E originated in Eurasia as E1b-M123 existing in the Levant in 2000 AD.

We need older samples, from Africa and Eurasia, because E is over 50,000 years old. There's a little known study with 6,000 year old Y DNA from Sudan which is mostly DE(not tested for E).

1. Admixture did not only occur within the Near East but extended towards Europe. To the266 north, a population related to people of the Iran Chalcolithic contributed ~43% of the267 ancestry of early Bronze Age populations of the steppe.

2. While the Early/Middle Bronze Age ‘Yamnaya’-related group (Steppe_EMBA) is a good geneticmatch (together with Neolithic Iran) for ANI, the later Middle/Late Bronze Age steppe population(Steppe_MLBA) is not.

They suggest that the Steppe like ancestry came to India from the Steppes in bronze age , But ANI is clearly older than any such date, its now clearly indicated. They say it ONLY because they assume such ''steppe like'' ancestry did not exist in S Asia before bronze age. Its going to be proven that such ancestry was present in SC Asia , and population from that area migrated both to India and Europe!.

It just means that they need more samples. A lot of the language in this paper (and that new Native American overview paper) are making it clear that there is often more than one way to analyze genetic data.

The authors know that they could be wrong, so they use language to reflect the uncertainty.

In the case of the circular ancestry, they need older samples to decide which is correct.

"They say it ONLY because they assume such ''steppe like'' ancestry did not exist in S Asia before bronze age."

That is just crazy. Just because all of the data that they actually have suggests this, they keep assuming that their data reflects some actual history. Have you sent them your email address? Maybe they are unaware of all the data you have been collecting independently.

"I would say that judging by what we know about places with much better sampling, then it is way too simple."

Maybe too simple, but Im not often wrong.

That we see the most basal lineage is the Iran Mesolithic instead of (the even older) Natufian is clear cut: BE cannot have come from northern Africa directly. But somewhere surprisingly further east, well inland in western Asia.

It may or not be too simple, but there's been a lot of evidence that Basal formed, or at least expanded from, the Gulf area. A recent case that makes a good claim based on R0a2: Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes http://www.nature.com/articles/srep25472

To get really spacey, it's possible that Basal descends literally *from* the Gulf, before it was flooded. That would explain similar flood myths that arise across otherwise disparate but Basal-rich areas.

This paper didn't even investiagte very much the relationship between ancient and modern genomes. I don't blame them at all. But anyways here are some specualtions about the modern affinities of Natufians

Everything from this paper was 100% expected. Natufians in my opinion will turn out to be the primary ancestors of SouthWest Asians and North Africans. I see evidence of this in mtDNA/Y DNA not just PCA, F4-stats, etc. However Sardinians are probably their closest living relatives, because of African admixture in SouthWest Asia/North Africa.

Natufians and Neolithic Turkey are closely related. Natufians are not ancestral, at least to a large degree, to Neolithic Turkey though. They're just close relatives. This is SouthWest Asians, like Bedouin, have been modeled successfully EEF.

I wouldn't be surprised if Natufians were Afro Semetic speakers because everyone who speaks a Afro Semetic language has loads of Natufian-related ancestry(including Eastern Africans).

As regards their comment on the ANI ancestry of South Asians, is it possible that they descend from the inhabitants poltavka and Andronovo represents an extinct related population? Andronovo appears rather late to be an ancestral settlement to the indo-aryans

Come on Krefter. We all you that you are omnipresent, but even you did not expect >99.9% of this paper.

They didn't go into comparison with modern populations because these authors tend to get 3 or 4 major publications out of each new data set. It is good for their funding, which is good for the rest of us. (No matter how screwed up the funding system is).

They say early bronze age steppe folks and ANI have close affinity . They say that late BA steppe folks don't have such affinity ! . They concur that by getting aDNA from ''South of Steppes'' will resolve the issue !.

That's what it is.

Getting the aDNA from SC Asia , then we can talk about data concluding the things.

With all this extra data, it also proves beyond doubt that Sintashta-Andronovo is from eastern Europe, given that it is steppe with distinctly European middle Neolithic, nor Levant, Anatolian or Iranian.

I discussed the problem of the current Andronovo and Sintashta samples not being very good references for steppe admixture in South Asia in my Srubnaya outlier post.

http://eurogenes.blogspot.com.au/2016/04/the-srubnaya-outlier.html

Basically, it seems that Z93 and Indo-Iranian languages spread from the Ural steppe with a population with a higher ANE ratio than the Andronovo and Sintashta samples we currently have. This population may have been very similar to one of the samples in the Srubnaya sample set.

@Karl_K,"Come on Krefter. We all you that you are omnipresent, but even you did not expect >99.9% of this paper."

Yes I am omnipresent and knew what the results would be because, yesterday I was hanging out with my Natufian and Zagros pals, that's how I knew what the results. I'm their Fire God.

No actually coincidentally yesterday I visited the Oriental Institute at Chicago University yesterday. It's a world-class museum on the ancient Middle East and includes a lot of artifacts from the Paleolithic and Neolithic.

I think we'll see confirmation that CHG/ Zagros is in Anatolians, but more Natufian to Anatolian in Spain. It was fairly easy to put CHG in LBK and Hungary before this and it should be easier now. Hopefully, the data is released soon.

I'm leaving for work in a moment, so I can't say much. I'll read this thing in detail much later (so much to digest). Anyway, I can't believe so many questions just got answered in this paper, tremendous stuff.

But just to get it out there, finally, it's good to see that the whole debate concerning the LN/EBA European genetic contribution to Central Asia/South Asia is finally over. The Kalash are 50% something very similar to Northern Europeans (and Pashtuns are fairly similar), in the words of this paper. It's funny looking back, at how contested this was.

In addition, it seems my notion concerning Balochistan was correct, but I had the wrong Baloch populations in mind. It seems Makranis (who are really coastal Baloch. Makrani is a confusing label, also applied to Balochi-speakers of predominantly African descent) are pretty much overwhelmingly Iranian Neolithic, although I'm sure there are more inland Baloch tribes who can also be construed as such. There is going to be genetic structure in such a tribal region.

For South Asian admixture, they're pretty clear that the ANI is Iranian Neolithic + some steppe. It's curious & probably significant that South Asians are modelled as Neolithic Iran, rather than Chalcolithic Iran. If correct, then it means that Iran_Neolithic was probably present in South Asian already since the Neolithic, and the only "new" component is from the steppe? (albeit potentially carrying Chalcolithic Iran stuff)

This statistic is 1 or more for non-Africans without African, and even some with a little of it like Jordanians. It is also >1 for Iranian Neolithic who have less Neanderthal admixture and more "basal" according to the paper, in fact it's almost identical for Iranian and Anatolian Neolithics..

The Chl Iranians are probably why there is inflated steppe ancestry in lot of those South Asian groups. Once the Genomes of those Rakhigarhi samples are out, that will explain that well. Now I am starting to think the BMAC was populated by Chl Iranians, which would make sense as proto BMAC was derived from cultures along the Caspian.

Just noticed this existed basically 30-45 minutes ago. So many answers will be in this.

Initial reactions:

The huge implication is that we now know we have at least two "Neolithic Dawns" in West Eurasia, initially apparently genetically separated.

More work will be needed (and hopefully there are fossils) to learn if these were truly totally genetically separated, or whether the Levant Neolithic and Iranian Neolithic involved some degree of genetic exchange (by populations yet more isolated than the Neolithic Levant and Iranian here).

We also see now that the south of West Eurasia was also beginning to merge, during the Bronze Age, in the same way as the north of West Eurasia. There is a broader dynamic here

However, before I get down to reading for anyone who has read and understood, do these big questions remain?:

- Did the Natufians or Levantine Neolithic populations contribute to the Anatolian Neolithic at the right time frame, or were they a separate population? I.e. were the Levantine farmers bringers of the Neolithic to Anatolia, or were they a structured population that developed it at the same time, using trade, like the Neolithic Levant and Iran are).

(If so, it looks at least from their ADMIXTURE like after the Levant Neolithic populations are considered, the ultimate "genetic survival" by the broader WHG-Villabruna clade may be much more comparable to EHG than we thought! Although the contribution by the West European members of the clade would still be low.)

(Another aside, the pattern of the position of BedouinB on that PCA makes you wonder what will happen if with ever get Neolithic Arabian dna. Though with this paper that's not an *if* anymore, it's a *when*).

- Just from PCA Chalcolithic Armenia perfectly overlaps early and late Bronze Age Armenia. So was there *any* population change there? Chalcolithic Aremnia is contemporaneous with Yamnaya btw.

- There doesn't seem to be any immediate problems, from PCA and ADMIXTURE, with modeling Yamnaya as Iranian_Neolithic + EHG (and also CHG the same way). Is this truly the case, or is there detail in the paper that contradicts this (and actually makes a case for Yamnaya as CHG+EHG)?

Essentially the question here is "Is there an excess of sharing by Yamnaya with CHG over and above what would be expected for an EHG+Iranian Neolithic composite? Or even is the opposite?".

(Now I do fully expect that Georgians *will* have an excess of sharing with CHG over and above what would be expected for a CHG proxy of Iranian Neolithic plus EHG.)

He said above that European mt not belonging to hg. U are at 99% of Middle Eastern Origin. First of all he could say what is Middle East, seen that also for the Y Israael/Jordan are very different from Iran and more from Northern Turkey practically similar to European hunter-gatherers. The "Natufian" mt have some subclades known also in Europe from so long (let's wait that Italian mt is tested as Italian Y, and Balkan one etc.) For instance there is a sample of K1a4b, with descendants in Middle east to day, but K1a4 is very likely older in Italy, and the same from other haplogroups, who may come from the Caucasus better than from "Middle East". Also about the origin of R0a2 and its ancientness in Italy I have written a lot, and so on.

Of course it is very likely that those haplogroups present in many Jewish lineages all over the world have more probability to be Old Jews rather than those haplotypes with a MRCA after the diaspora, that my opponents say due to a bottleneck and I say due to introgression. Very likely hg. E is the oldest in Middle East and perhaps in oldest times the unique. Of course J arrived not more than 5000 years ago, and also these hgs may be old in Jews as also many R1b, but so far from the R-M343 tree of Sergey Malyshev only a few subclades seem old in Jews. We'll see from the next tests and above all from aDNA.

- The very high Basal Eurasian estimate in Mesolithic Iran suggests that Iranian Neolithic and Levant Neolithic may already have begun to mix with one another and the European / Siberian HGs?

- Natufians are probably going to be a very structured (North) African population, aren't they? Basically. One that no longer exists. As "no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians".

Yet Basal Eurasian is clearly quite ancient in the ME, and seems present before an Natufian incursion - "The idea of Natufians as a vector for the movement of Basal Eurasian ancestry into the Near East is also not supported by our data, as the Basal Eurasian ancestry in the Natufians (44±8%) is consistent with stemming from the same population as that in the Neolithic and Mesolithic populations of Iran, and is not greater than in those populations"

(which is a strike against the idea that Natufians themselves brought a set of farming pre-adapted genes into the ME, which spread with BE).

- Regional differentiation in the ancient Middle East seems more intense than between European and Siberian HGs. Particularly relative to the extremity of low population size.

So, all the findings where unsupervised ADMIXTURE kept digging out a West Asian, Levant-Mediterranean and "European" cluster (and then splitting the Levant-Mediterranean into West Med and SW Asian), rather than WHG, ANE and ENF were perhaps closer in a sense closer to the truth we find now than our supervised models after Laz 2013, where we were trying to force a model of WHG, ANE and ENF.

- The estimates of steppe ancestry in South Asians seem extreme, however, if you work from the assumption that Iranian Neolithic is more "extreme" than CHG and CHG is already admixed with EHG, that may help them make more sense. I'll be interested to see Davidski's modeling on this.

It does suggest that it's less likely that many present day "Northern European" traits (tall height, unusual pigmentation) actually spread with steppe ancestry though, if true. Or were *strongly* selected against.

- "We also document a cline of ANE ancestry across the east-west extent of Eurasia. Eastern Hunter Gatherers (EHG) derive ~3/4 of their ancestry from the ANE (Supplementary Information, section 11); Scandinavian hunter-gatherers7,8,13 319 (SHG) are a mix of EHG and WHG; and WHG are a mix of EHG and the Upper Paleolithic Bichon from Switzerland (Supplementary Information, section 7). Northwest Anatolians—with ancestry from a population related to European hunter-gatherers (Supplementary Information, section 7)—are better modelled if this ancestry is taken as more extreme than Bichon (Supplementary Information, section 10). "

No comment necessary. :)

... Well, actually comment is necessary, isn't it? They need to validate this against the findings in Fu et al 2016, on Ice Age Europe, which they've controlled for to some degree (e.g. using Ust Ishim as a validator for BE as they should, and not using ENA) but not really included in a robust sense. Fu et al has much broader scale groupings from the Villabruna cluster and evidence for admixture in some Villabruna by El Miron cluster (the Magdalenians).

"Natufians are probably going to be a very structured (North) African population, aren't they?"

Quite possibly. Also even though direct Chimp SSA X Y doesn't seem to detect it here (ascertainment?), fst-ratios I posted earlier imply some connection to SSA, even relative to modern Near Easterners and ancient populations that supposedly have as much or more basal than Natufians.

Agree with upthread comments that they really should be modeling with later Iranian population and Chalcolithic Armenia as well, as much as still not 100% about qpAdm as a method. It would've been nice to have an ADMIXTURE based method (and perhaps f4 ratio as well) comparison as a "sanity check" here, as in the Cassidy et al (Bronze Age Rathlin paper).

(And generally, why no ADMIXTURE of the modern world dataset plus ancients?).

- Their qpGraph methods will benefit from being re-tested with all the Fu et al samples, not just Kostenki14 to check for consistency, since there's a cross historical timeslice there.

However, looks like they have one model Figure S4.11 that models Iran_Neolithic as EHG+Basal Euraian (38:62 ratio and plus lot of separating drift in Iran_Neolithic).

"This led us to try one last model in which we model Steppe_EMBA as a 3-way mix of EHG, CHG, and Iran_ChL. The P-value for rank=2 is 0.241, so 3 streams of ancestry are consistent with the quadruple (Steppe_EMBA, EHG, CHG, Iran_ChL) and the fitted mixture proportions are 52.7% EHG, 18.1% CHG, 29.2% Iran_Ch "some people just jumped on wrong conclusions merely out of the fact that they don't like the idea of Yamna possibly being from Iranian Plateau.

Even the sentence "no direct geneflow" should have made anyone suspecious that they don't exclude indirect geneflow.

It makes archeological 100% sense. Maykop culture is descend of the Layla Tepe culture which according to archeologists derives from the Iranian Plateau.

Am I missing something? Or did the outcome of the paper shocked you guys so much that you are in denial now? How "Bury" the Out of Iran theory "completely" now if the paper obviously points out that there was geneflow from Iranian Plateau into the Steppes and than we have a P1 sample that could be anything from R1(R1a,R1b), R2 to Q.

My theory is still that Indo European likely evolved in the Steppes but is a creol language that appeared out of a fusion from Iranian Plateau herders and EHGs.

@ SamYou know me very well, and you could spoke to me and not to an anonymous, but remember what I said: that Jews aren't sure to descend from Old Jews neither when they are hg. E or J. All your Stanford's PhD-s have been definitely defeated by me.

@ Azarov DmitryWhere have you seen in these data that R1b and R1a came to Europe from the Iranian plateau? That P* haplotype doesn't demonstrate anything and at least it is R2 as Davidski said too. I remember you that R1b1a has been found in Villabruna, Italy, 14000 years ago and many R-L23 subclades in Samara, Russia.

Not surprising at all. H was found in Neolithic Anatolia and if i remember it correctly also among European Neolithic Farmers which both lacked any South Asian admixture. H has probably a very complicated history could be Basal Eurasian or like IJ some Hunter Gather lineage which spread over vast tegion and was absorbed byfarmers

Two things.1. proves haplogroup J2 comes from the Caucasus, not the Levant. All Levantine farmers lack J2.2. "Steppe ancestry" will get bloated in Iran and South Asia unless we can get an idea of how much CHG like ancestry in South Asia and Iran is from the steppe and not earlier migrations. The Neolithic Iranians are very much like CHGs.

It must really, really suck to be an OIT supporter right about now.Whenever Harrapan Y-DNA is finally released, and there's no R1a, are you going to actually make good on your promise(made last year on this blog) to go away? Or are you just going to keep making dumb rationalizations?

The moment the antis have no more arguments left, they make just some very weird statements.

Dave Who said ancient the Near East was full of R?? Do you actually read comments? I always said we will find R Haplogroups on the Iranian Plateau, as well South_Central Asia, prior to Bronze Age. I was confirmed. Thats it no more need for talk

The comment section for this blog is a magnet for nut bars. Funny how commenters here believe this pre-print supports their stance on the IE issue, regardless of whether they support the Kurgan theory, a Near Eastern origin, Central Asian origin or the zombie OIT.

The Y data defined as CT is frustrating but it appears that G and H2 (old F) were the predominant groups of EEF and the eastern Iran types were J1/J2 who pushed westwards and/or were jockeying for territory. E1b were hunter gatherers of the Levant who appear to have adopted farming from the G/H2 guys who were based out of western Anatolia. Depending on what exactly CT is, L and T fit in there somehow as well...of course small numbers of hunter gatherers R and I were probably in southern Europe and may turn up during the Neolithic Near Eastern period as well. I suspect most of the R found in the Near East is of Late Bronze Age or Iron Age period.

E1b adopted farming from Anatolians? Idk about all that but the Natufians developed quite a few things independently of their northern neighbours, and were settled before agriculture even developed in their area.

If the Iranian samples had come back with substantial amounts of Y-DNA R1, then maybe the idea of an Iranian PIE homeland would be more likely.

I do not think it probable that a people who spoke a language (PIE) with words for bride price, son's wife and brother's wife but not words for daughter's husband or sister's husband spread said language via female exogamy.

Not impossible, but if someone put a gun to my head and told me to choose the PIE Urheimat, it still wouldn't be the Iranian plateau.

So I have some questions now about Neolithic Iran. Since they're related to CHGs can we say that they are the product of CHGs migrating South, since we know CHGs are native to Upper Paleolithic Georgia since at least 11,000 BC. Or is it that you guys think they were always in Iran? Could they have been present in Northern Iran for as long as their relatives were in Georgia?

At page 8, lines 265-267: "To the 266 north, a population related to people of the Iran Chalcolithic contributed ~43% of the 267 ancestry of early Bronze Age populations of the steppe."

The short answer is that EHG and Iranians contributed roughly equally to the Bronze Age steppe population which either included or was immediately descendant from the Proto-Indo-Europeans. So, you're both wrong.

It looks like CHG-related populations lived in Iran as far back as the Ice Age. They weren't CHG proper, but closely related.

However, it seems that there was a rush of this type of admixture from somewhere in the north, probably CHG proper from the Caucasus, into Iran during the Chalcolithic.

This matches archaeological data as far as I know.

It's possible that the same groups that moved into Iran made some sort of impact on the steppe as well, especially if they were expanding from the Caucasus. But if they did, it was via female exogamy with steppe people.

Nonetheless the 3-way model is also plausible as it suggests an explanation for the shared genetic drift between Steppe_EMBA and the Anatolian and Levantine Neolithic (underestimated when CHG alone is the southern population; Table S7.12), and makes geographical sense as admixture from the Near East could have arrived on the steppe via the Caucasian isthmus where an addition of CHG ancestry could have occurred.

In other words, you shouldn't take the main models too literally, even if they're statistically most parsimonious.

There's actually no direct evidence in this paper that anyone from Iran ever made it onto the steppe during the Chalcolithic or Bronze Age. Not an iota.

And I'll also add that in my opinion Steppe_EMBA is really a mixture of EHG, CHG and Chalcolithic Balkans.

'R1a-M417 and R1b-M269 obviously expanded from the Eurasian steppes during the Bronze Age. And that essentially solves the Indo-European question.'

What if they spread from there but were not Indo-Europeans? Scythians even had a kumis-like dairy product. The word 'Kipchak' means blonde Saka. 'Yakuts' identify as Saka. Greeks called Pechenegs and other Turkic and Hunic groups 'Scythians'. In an Armenian chronicle Pechenegs are descibed as an 'all archer army'.

[QUOTE] An interesting aspect of this model is that it derives both Natufians and Iran_N from Basal Eurasians but Natufians have ancestry from apopulation related to WHG, while Iran_N has ancestry related to EHG. Natufians and Iran_N may themselves reside on clines of WHG-related/EHG-related admixture. The fact that these two populations are differentially related to European hunter-gatherers can be directly seen from the following statistics:

MA1, EHG, SHG, Switzerland_HG are consistent with having no Basal Eurasian ancestry, while at least some such ancestry is inferred for the remaining populations.Neolithic Iran and Natufians could be derived from the same Basal Eurasian population but are genetically closer to EHG and WHG respectively We take the model of Fig. S4.9 and attempt to fit Natufians as a mixture of the same Basal Eurasian population that contributes to Iran_N and any other population of the tree. Several solutions are feasible, and we show the best one (lowest ADMIXTUREGRAPH score) in Fig. S4.10. We can add both EHG and MA1 as simple branches to the model structure of Fig. S4.10 and show the results in Fig. S4.11. An interesting aspect of this model is that it derives both Natufians and Iran_N from Basal Eurasians but Natufians have ancestry from a population related to WHG, while Iran_N has ancestry related to EHG. Natufians and Iran_N may themselves reside on clines of WHG-related/EHG-related admixture. The fact that these twopopulations are differentially related to European hunter-gatherers can be directly seen from the following statistics: suggeststhat the singleton individual from Hotu (Iran_HotuIIIb) was shifted towards EHG along the Iran_N/EHG cline, albeit it does not reach |Z|>3. There is uncertainty about the date of Iran_HotuIIIb, as it is not certain that it is of Mesolithic age and thus predates the Neolithic of Iran from Ganj Dareh.The fact that the Caucasus hunter-gatherers (CHG) (who are definitely pre-Neolithic) have extra EHG-related ancestry is also supportive of a substantial antiquity of this element in the Caucasus-Iran region. It is not clear whether the hunter-gatherers preceding the Neolithic in Ganj Dareh were similar to Iran_HotuIIIb or the CHG and their EHG affinity was diluted during Neolithization, or whether they are descended from an unsampled hunter-gatherer population that already had this reduced affinity to the EHG....

Thus it is rather the Mesolithic of Iran that shares more alleles with these eastern European groups than the Neolithic. Tentatively, this might suggest that the pre-Neolithic population of Iran had an affinity to the EHG/Ancient North Eurasians that was diluted during the Neolithic, although the lack of negative f4-statistics does not allow us to discern what is the source of this dilution. Alternatively, there was no dilution, but the Neolithic of Iran was descendedfrom an unsampled Mesolithic population.[/QUOTE]

Seems like the paper does "confirm" another of my theories, namely that before Neolithic (possibly even a little earlier) the Iranian Plateau was populated by a very ANE like population, than this ANE like population mixed with an "incoming" population (Basal Eurasian?) that brought farming to them and is the reason why Iranian Farmers are more Basal Eurasian than CHG which seems to be the "only" difference between both groups.

This same "Basal Eurasian" population seems also to be the one who brought farming to Natufians. Because Natufians are basically Basal Eurasian and something WHG like.

With other words EHG seem to have Iranian mesolithic ancestry minus the Basal Eurasian.

"There are numerous cases where the language of the females becomes dominant eventually. English is the best example against both the Scandinavian males and French speaking Normans."

Language change doesn't necessarily involve any significant change in DNA, and are more the result of socio-political changes, but just for the sake of argument, trying to paint Anglo-Saxon linguistic survival as female linguistic dominance is hilarious, as most female lineages in Britain are liable to have been pre-Anglo-Saxon.

In fact, Scandinavians [Vikings] and the Normans had very limited genetic impact on the population of England whilst the Anglo-Saxons, the actual forebears of the English language, had a significant impact, estimated at 30% by Leslie et. al (2015). English is a Germanic language, and the Y-DNA of Englishmen contain a significant percentage of R1b-S21/U106, which has been called "Germanic" by not a few scholars. Thus, even were to examine the English case, the theory falls apart.

This also applies to the rest of the people trying to associate early Neolithic population movements with linguistic lineages. Even proto-Indo-European isn't that ancient, and the same is probably true of proto-Afro-Asiatic. The paper is of no great surprise to me, but then I've always assumed that R1a/R1b did not come from the Near East. It's nice to see a bit of evidence. And I fail to see how it changes the popular view of proto-Indo-European history, though I might be behind on that.

"There's actually no direct evidence in this paper that anyone from Iran ever made it onto the steppe during the Chalcolithic or Bronze Age. Not an iota.

And I'll also add that in my opinion Steppe_EMBA is really a mixture of EHG, CHG and Chalcolithic Balkans."

The fact that you prefer a less parsimonious explanation than the one given in the paper as its primary hypothesis does not justify dismissing the paper's primary hypothesis out of hand with a "nope". Also, it is a straw man to say that no individual from Iran ever made it onto the steppe during the Chalcolithic or Bronze Age, although I'm sure that at least a few did.

The hypothesis supported by the genetic data instead is that 43% of steppe is derived from the Iranian Chalcolithic. It is entirely possible that this could have occurred over several generations of intermediate migration via either the Caucasus or Central Asia.

In particular, the hypothesis the Chalcolithic or Bronze Age Caucasians contributed to the Steppe population has ample archaeological and historical linguistic support, and the hypothesis that Iranian Chalcolithic populations were an important source population for Chalcolithic Caucasians likewise has archaeological and historical linguistic support.

Indeed, the genetic evidence in this paper tends to show, roughly speaking a three gene pools of early farmers - Levantine, Anatolian and Iranian (to oversimplify) and there is ever reason to think that the famers and pioneering metallurgists of the Caucasus had little demic contribution from the Levatine cluster and a lot of contribution from the Iranian cluster.

The archaeological evidence also makes no very persuasive argument for preferring a Balkan source (where metallurgy developed a bit later and where Kurgans type burial practices were a fairly late development) to a Caucasian demic contribution (where metallurgy developed a bit earlier and where there is continuity of Kurgan-like burial practices) to the Steppe people in the Chalcolithic and indeed the genetics seem to favor a Caucasian source which would be more Iranian-like to a Balkan one which would be more EEF/Anatolian-like as a demic contribution.

While I recognize that you are thinking of CHG in terms of a genetic component, rather than a true archaeologial culture, it is also pretty clear archaeologically, the Steppe people received much of their technological package from a farming and metal using culture and not from actual hunter-gathers. Indeed, I'm not aware of any evidence to support the idea that there were still any hunter-gatherers in the Caucasus by the Chalcolithic, even if the local farmers may have had significant genetic continuity with the hunter-gatherers that preceded them in the area.

Even though it was already obvious, this paper has shown that the Steppe peoples migrated from Eastern Europe into all of the IE speaking areas (Europe, Middle East, and South Asia). Clearly these steppe people are the last link we have between all IE people. They must be the PIE people.

To those that still want to find wiggle room, you can't. The PIE problem is effectively solved. The last link between IE peoples are these Steppe folk. By definition that is PIE...

For anyone who wants to talk about Pre PIE... If it is a thing, I would side with david in thinking that it wasn't Caucasus/Iranian women who brought their language to the steppe and then the steppe people moved into the middle east and erased all evidence of this pre PIE language. You would think that if pre PIE was actually carried by iranian women, some remnants of pre PIE would have survived in Iran and India. If pre PIE did exist, it likely succumbed to a local development of PIE.

""My theory is still that Indo European likely evolved in the Steppes but is a creol language that appeared out of a fusion from Iranian Plateau herders and EHGs."

Bro- PIE isn't a creole. There are technical reasons which I won't go into, but it's not really too debatable . IE is a 'normal' language "

All languages come from somewhere, and not necessarily in a pure tree-like evolutionary form. Kurti's articulation of Indo-European as a technical "creole" may not be true in the narrow sense, but it is sensible to believe that Indo-European ethnogenesis took place on the steppe and that the language spoken by the newly arising culture is not a straightforward direct daughter language of either the LBK farmers or of the hunter-gatherers who inhabited the steppe before them, and there is archaeological evidence of communities on the steppe at the estimated time of Indo-European ethnogenesis that had ethnically mixed populations that drew on both farmer and steppe hunter-gatherer populations. So, it isn't unreasonable to think that more than one language family made meaningful lexical, phonetic and grammatical contributions to Proto-Indo-European.

Perhaps a better technical description of the formation of Indo-European may have been that there was a superstrate parent language and a substrate language whose relative status levels where so nearly equal that it was hard to tell which was which from subsequent linguistic data resulting in a maximal substrate linguistic influence.

The process might be compared to a more extreme version of the process by which the Japanese language family came to be with a primary source that was probably a language of an ancient, probably now extinct Korean language family, but with such heavy lexical and written language contributions from Chinese that Chinese is, if not is mother, at least its step-father.

As some other examples, Dravidian languages had not just lexical but strong grammatical and phonetic influences on Hindi as a substrate language, and the Semitic Akkadian language had strong grammatical and phonetic influences on Sumerian before it superseded the Sumerian language entirely.

"Even though it was already obvious, this paper has shown that the Steppe peoples migrated from Eastern Europe into all of the IE speaking areas (Europe, Middle East, and South Asia)."

This paper presents no new samples from Europe, so insofar as that question is answered, it isn't from this paper, but from earlier ones. Still I do have to agree, given that we now have samples from both Ice Age Europe and the Neolithic Near East to support the scarcity of R1a/R1b outside of Eastern Europe. But it could also be that R1a/R1b were simply rare before a certain explosive expansion period, and were confined to regions that have not yet been sampled; we'll need early Neolithic samples from Eastern Europe to corroborate the idea that it was the R1a/R1b homeland, so the verdict is still out.

"Iranocentrist said...Yes it is quite obviouse now that Iran was the source of steppe IE's."

Do you realize that you are basically only arguing where Pre PIE came from. The last shared heritage of all IE peoples is the steppe. The most recent common ancestor is what makes something "proto". Iranian and Indic came from the steppe. You can try to argue that pre PIE came from Iran... but Iranian came from the steppe.

@lathdrinor "This paper presents no new samples from Europe, so insofar as that question is answered, it isn't from this paper, but from earlier ones."

True, but we now know Iran didn't harbor any EHG or steppe like signature prior to the bronze age. We can extrapolate that there was not EHG gradient that went south of steppe prior to the enolithic. Therefore, the steppe like signature in indians came from the steppe.

On PIE being normal and not a creole. I am neutral on the subject but all languages are pidgins then creoles to some extent especially at the beginning. and I don't understand such a rigid classification. English and other languages IE seem to have creole elements.

Similarly DNA and social groupings would work in a similar fashion. Zorastrian/parsi DNA is modern but somewhat eye opening and something I never looked at before. I assumed they would have higher R1a than fellow Iranians, but they don't.

Its a snapshot of an old IE speaking community. they would have a growth phase attracting new converts and DNA, a stable endogamy phase and then decay after islam. What it tells us is that not all IE speakers had R1 ydna. While this may seem unremarkable, we see too much of these blanket assumptions nowadays.

As for R lineages in western Iran I think they will be found in similar proportion to what is found there today, Lets see.

"On PIE being normal and not a creole. I am neutral on the subject but all languages are pidgins then creoles to some extent especially at the beginning. and I don't understand such a rigid classification. English and other languages IE seem to have creole elements. "

Well, these 'rigid' classifications exist to clarify the social aspect of language inheritance. Its does make a difference, if details matter to you.

Creoles are unusual events, they happen in modern Colonial period when a whole bunch of people are forcibly lumped together. As Andrew stated, this is different to language shifting and inherited substratum effects.

the greeks don't really matter. Italo-celtic, iranian, and Indic are only connect by PIE. There last genetic connection, the steppe, is strong and has the timing of PIE. Therefore the steppe needs to be PIE. If greek lacked steppe, then I would just say that the greeks were language converts.

You can still make the argument that anatolian was the original early PIE, then its daughter, late PIE, moved into the steppe explaining the steppe connection between enland and india but the anatolian hypothesis is already debunked imo.

"What is a "language convert ' ? Is it something like western champagne liberals suddenly becoming Buddhist & vegan ?"

I imagine it's similar to being a religious convert - more culture, less genetics. And there certainly are examples of language converts. India and English being an example, as despite the Indo-European link, we can safely say that India was not English speaking prior to the British Empire, and that the situation today was not the result of significant English genetic impact on Indians.

The hypothesis supported by the genetic data instead is that 43% of steppe is derived from the Iranian Chalcolithic.

Nope, the hypothesis supported by the genetic data is that ~43% of Steppe_EMBA ancestry is related to Iranian Chalcolithic.

Big difference, and a problem, because Iranian Chalcolithic is different from Iranian Neolithic.

@Lathdrinor

But it could also be that R1a/R1b were simply rare before a certain explosive expansion period, and were confined to regions that have not yet been sampled; we'll need early Neolithic samples from Eastern Europe to corroborate the idea that it was the R1a/R1b homeland, so the verdict is still out.

And who were the Khvalynsk men? Migrants from Iran? Because to me they look a hell of a lot like native Eastern Europeans.

Yes we can all imagine what a language convert might entail, but my sarcasm was merely pointing out the absurdity of such an idea.

Wishy-washy colonialist analogies do not suffice for a vastly different period, in a different place. Industrialist England and their colonization of the subcontinent is irrelavant for the Copper Age interactions across Europe, the steppe & near East. Same deal with all the misguided use of America & the fate of its natives

Bronze Age Anatolia was teeming with IE speakers. The Myceneans were obviously also IE. Now, given that these regions were densely populated, and had developed heirarchical systems already by late M4, why should they 'convert' all of a sudden to the language of some fledgeling cattle-herders from the steppes ?

The only way this "conversion" is possible, is by outright colonization- at some point between 4000 BC and 200o BC. Which is to say, not a 'conversion' event at all.

So we should expect to see steppe admixture in EBA- MBA Greece & Anatolia

"And who were the Khvalynsk men? Migrants from Iran? Because to me they look a hell of a lot like native Eastern Europeans.

http://eurogenes.blogspot.com.au/2015/11/the-khvalynsk-men.html"

They do, but where did they come from, and were they the only R during the period? After all, we have an Epigravettian R1b from Italy to consider, from Paleolithic contexts. If R1b could spread all the way to Italy during the Paleolithic, it could've spread to other regions before the Bronze period, in which case the question is: where and from where? It is not yet time to say that Samara/Khvalynsk was the *only* center of R1 during the Neolithic. Those cultures may have played a huge role in the distribution of R1 today, but they may not have been the earliest homeland of R1 and they may not have been the only regions from which R1 spread. To me the Khvalynsk sample serves more as a repeat of the Yamnaya evidence, indicating that the Volga region was in fact an early center of R1, but not necessarily the only one.

We've come along way from Basal farmers from the Levant spreading everywhere over local HGs.

I think we're partly looking at a recurring pattern of early farmers creating their own nemesis i.e. they expand to the border of farming viability and beyond that border they catalyse HGs into pastoralists and eventually the pastoralists beyond the border get strong enough to come over the border and destroy /displace the farmers.

#

"a population related to people of the Iran Chalcolithic contributed ~43% of the267 ancestry of early Bronze Age populations of the steppe"

related to, not same as

somewhere in between which expanded both ways might be Caspian coast?

#

a population with a military edge can defeat a larger population - so hypothetical

Fascinating paper and fascinating thread. I love to read this blog because of the papers it features and the bloggers' comments, even if any R1b that pops up in a non-Steppe region will always be identified as a stubborn Steppe guy who got lost, refused to ask for directions and ended up far from home

Quote from Davidski."Just take a look how the Y-chromosome landscape of the Near East changed from the Neolithic to the present.

Y-HG R1 made a fairly big impact"

You got to hammer this into your minds. Western Asia isn't the home of R1 we, included myself, thought it was. It's at the receiving end just as Europe is.

Most R1 in the Western Asia is either R1a-Z93 or R1b-Z2103, both of whom have been found on the Steppe. The Basal R1s do exist in Western Asia but are a small minority. R1b-V88 in the Levant is another story.

The mystery of the origin of 90% of modern R1 is solved. It's from young(less than 8,000 years old) founder effects that occurred around Russia and Ukraine and then expanded in the last 5,000 years.

I could interpret your nickname as "Latrus", Latrus idearum mearum. This is my theory of an "Italian Refugium from at least 10 years. Anyway I thank you, because you are becoming in understanding the truth that pretty all the others, above all the PhD of Stanford and elsewhere, are trying to hide.

Lathdrinor has left a new comment on the post "The genetic structure of the world's first farmers...": "And who were the Khvalynsk men? Migrants from Iran? Because to me they look a hell of a lot like native Eastern Europeans.

http://eurogenes.blogspot.com.au/2015/11/the-khvalynsk-men.html"

They do, but where did they come from, and were they the only R during the period? After all, we have an Epigravettian R1b from Italy to consider, from Paleolithic contexts. If R1b could spread all the way to Italy during the Paleolithic, it could've spread to other regions before the Bronze period, in which case the question is: where and from where? It is not yet time to say that Samara/Khvalynsk was the *only* center of R1 during the Neolithic. Those cultures may have played a huge role in the distribution of R1 today, but they may not have been the earliest homeland of R1 and they may not have been the only regions from which R1 spread. To me the Khvalynsk sample serves more as a repeat of the Yamnaya evidence, indicating that the Volga region was in fact an early center of R1, but not necessarily the only one.Though it might have been the only one that mattered. We'll see.

As fas as I can see is that 1 out of 1 Neolithic Iranian sample is P (likely R1b) so, how can someone claim that R1b don't came from the Iranian Plateau? What we will see if we test 5 more ancient remains? Perhaps, other P (R1b) groups? Perhaps, the source of Western R1b.

Also interesting to see that I1707 is negative for T1a1 when I0795 from the ancient Europe is positive for T1a1. This mean that the Levant isn't the source for T1a1 in the ancient Europe, they both share common ancestor as far as 20000ybp.

Wishy-washy colonialist analogies do not suffice for a vastly different period

You are missing the point. It is easier to explain the greeks as having learned a language from steppe people rather than any other alternative. Thats all I'm saying. You should know the Greek is actually a language that branched off after Italo celtic but not before Indo Iranian. If you think that PIE wasn't steppe then explain how steppe manage to get into Italo Celts and Indo Iranians but not the greeks? Again, the latest linguistic connection between English and Indian is PIE and the latest genetic connection is steppe.

I expect the Greeks to have steppe ancestry but nothing fundamental will change if they didn't.

@Geo "It is not yet time to say that Samara/Khvalynsk was the *only* center of R1 during the Neolithic. "

It is the center for m269, which has to do with the IE question. I have no idea how r1b came into western russia. I doubt it was via the middle east or we would have seen a lot more r1b in neolithic samples or a lot more in india.

Greeks have Steppe ancestry. Current estimates have it varying from 20-30% in Greece. That's not small at all. Steppe ancestry has definitely been in Greece since the Bronze age. We already have unpublished confirmation it was in Croatia back then.

@ Colin Welling"@Geo "It is not yet time to say that Samara/Khvalynsk was the *only* center of R1 during the Neolithic. "It is the center for m269, which has to do with the IE question. I have no idea how r1b came into western russia. I doubt it was via the middle east or we would have seen a lot more r1b in neolithic samples or a lot more in india.

Colin, at Samara we have only some subclades of R-L23*. There lack the upstream and the downstream subclades, thus there wasn't the origin of R1b1-L389 and subclades. Above all there hasn't been found R-L51, the ancestor of all the downstream subclades of Western Europe.As it has been found R1b1a* at Villabruna 14000 years ago, you will see, when these PhDs will decide to test other samples from Tyrrhenian Italy and other places of Western Europe where R1b migrated from the "Italian Refugium", where the R1b1a2-M269 was born. Your statement is based upon nothing.

No, you're missing the point bud. Im not saying that PIE didn't expand from the steppe, but you are inventing ideas about language switching without any explanatory details, as if by special pleading. What's more, the details of your vision of the tree are simply false, as Greek split more or less equally with IA & celtic. In fact, Greek is probably a lot older than Celtic. To top it all off, you come up with pearlers like "the latest linguistic connection between English & Indian is IE".

The early speakers of the Anatolian branch, i.e. the Hittites, Luwians and Palaics, do matter a lot, because by all accounts the Anatolian branch is the most divergent of all IE branches. This may be reasonably explained by the assumption that they split off before all other IEs split. (Although there are other, less plausible theories, like that they were more strongly influenced by the non-IE substrate than all other branches.) For that reason the genetic affinities of the early IE Anatolians do matter even more than the origin of the Indo-Iranians. Because even if all other IEs were from the steppe, if the Anatolians were not, then PIE wasn't from the steppe.

@ Simon_W"For that reason the genetic affinities of the early IE Anatolians do matter even more than the origin of the Indo-Iranians. Because even if all other IEs were from the steppe, if the Anatolians were not, then PIE wasn't from the steppe".

Just because Hittite retains laryngeals, and the unique IE language which retains laryngeals for what I know is Albanian, I think that the origin of IE should be westernmost than it is usually thought: the Balkans, and before also westernermost...Of course I think that from the steppes expanded the satem IE languages, but not the oldest centum ones.

@ Andres Folg "They use "downstream" for "R1b1a2" IF P1 is upstream "R1b1a2", P1 is upstream R1b, then R1b is a possibility for this sample.

Are they wrong?"

Of course you are right, and only the Bam file will say which is its subclade. That it could be an Hg. Q or R2 is more likely, but of course we may not exclude some form of R1b or why not R1a. It is right to wait that Genetiker or some other reads the Bam file when it will be at our disposal. But if R1b were in Old Middle East we should have found some sample of it, but so far nothing of nothing from Natufians to even Western Anatolians who were very likeleìy linked to Western European hunter-gatherers. But let's wait...

"but you are inventing ideas about language switching without any explanatory details"

If PIE was steppe, and greeks don't have steppe, then it was exclusively a language transfer. Thats just logic.

The point your are still missing, probably willfully, is that its much easier to explain away a hypothetical lack of steppe in ancient greeks with the kurgan hypothesis, than to explain steppe admixture in Italo Celts, Iranians, and Indians without the kurgan hypothesis. The Kurgan Hypothesis stands regardless of whether or not the early greeks had steppe in them.

I said Italo Celtic. Its pretty sad when you lose sight of an argument, make it about technicalities, but still get that wrong. The branch that led to Italo celtic is the third branching in the Ringe et al phylogeny. The point is that the greeks did not break off before the Italo Celts and Iranians differentiated from one another, which would have allowed the possibility for the latter two to "enter" the steppes after the greeks had already taken off. Didn't happen.

"For that reason the genetic affinities of the early IE Anatolians do matter even more than the origin of the Indo-Iranians. Because even if all other IEs were from the steppe, if the Anatolians were not, then PIE wasn't from the steppe."

You are correct. Thats why I said the greeks don't matter. The anatolians, on the other hand do matter. If they didn't have steppe dna then that would pose some problems for the steppe hypothesis and leave open the possibility that the earliest PIE didn't start on the steppe. Still though, the anatolian hypothesis has too many holes imo.

@Geo, What are you disagreeing with? L23 is the relevant r1b haplogroup for IE. It was obviously in the Yamnaya and the bell beakers who introduced steppe ancestry to western europe. Im sure L51 was also (western) steppe derived.

"@Geo, What are you disagreeing with? L23 is the relevant r1b haplogroup for IE. It was obviously in the Yamnaya and the bell beakers who introduced steppe ancestry to western europe. Im sure L51 was also (western) steppe derived.

Are you questioning if L23 was born around the steppe?"

Have I to take "Geo" as my name? In what yousay there are many presuppositions not demonstrated:1) that R-L23 is the relevant R1b haplogroup for IE2) that Bell Beakers derive from Yamnaya3) that R-L51 will be found in Western steppes, when I demonstrated that to-day the sister clade R1b-L51-PF7589 is pretty at o,oo% Easterward Italy.

river Volga while other turn all the way east moving around the east side of the Caspian sea and making a blob of R1b north of Iran and the other following the river or maybe a mix of the two just settle in the southern Caucasus to what is today South Georgia, Armenia and west Azerbaijan. Or maybe some actually came from much closer from the Dnieper basin and just crossed the mountains."

Since this is a speculative post... It looks like this P* was the part of the r1b moving east of the Caspian...going nothbound, crossing araxes river and settling in shulaveri shomu. Ok suits me. ;)